Issues with mesh deformation
Here's a before and after picture to illustrate what I mean. On the left is what happened when I tried rotating the left shoulder using the original vertex groups. On the right is what happened after I reassigned the vertices in the the following groups: abdomen, chest, left shoulder, left upper arm, left lower arm. Double check that you are not only assigning the vertices that you want in each group, but also removing the ones you don't want.